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Articles by A. Sali
Total Records ( 2 ) for A. Sali
  S. Hitam , K.L. Tan , R.K.Z. Sahbudin , M. Mokhtar , S.B. Ahmad Anas and A. Sali
  Research indicated that there is no proven cure for autism sufferers. Usually, implementing the appropriate treatment and education can eventually help the autism person to be integrated into their community. However, the conventional visual schedule and training system that depending on physical tool and toy bringing the difficulty on changing or update the picture, text and current using tool. Therefore, Digital Visual Schedule and Training System (DVST System) is developed as a user- friendly, interactive and flexibility system for children with autism. The inconveniency of traditional training program that depending on physical tool or multiple application software is improved by DVST system that provides a complete set of features and functions for the therapist and autistic children to carry out the administration work (for therapist-Server) as well as training program (for autistic children-Client) in a single application.
  M.S Madhusudhan , B. M Webb , M. A Marti Renom , N Eswar and A. Sali
 

Comparing the structures of proteins is crucial to gaining insight into protein evolution and function. Here, we align the sequences of multiple protein structures by a dynamic programming optimization of a scoring function that is a sum of an affine gap penalty and terms dependent on various sequence and structure features (SALIGN). The features include amino acid residue type, residue position, residue accessible surface area, residue secondary structure state and the conformation of a short segment centered on the residue. The multiple alignment is built by following the ‘guide’ tree constructed from the matrix of all pairwise protein alignment scores. Importantly, the method does not depend on the exact values of various parameters, such as feature weights and gap penalties, because the optimal alignment across a range of parameter values is found. Using multiple structure alignments in the HOMSTRAD database, SALIGN was benchmarked against MUSTANG for multiple alignments as well as against TM-align and CE for pairwise alignments. On the average, SALIGN produces a 15% improvement in structural overlap over HOMSTRAD and 14% over MUSTANG, and yields more equivalent structural positions than TM-align and CE in 90% and 95% of cases, respectively. The utility of accurate multiple structure alignment is illustrated by its application to comparative protein structure modeling.

 
 
 
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